Hydrogel Microdroplet-Based Digital Quantitative Polymerase Chain Reaction

Abstract

Droplet digital PCR (ddPCR) is accurate in nucleic acid quantification owing to its linearity and high sensitivity. Amplification of nucleic acid in droplets, however, is limited by the stability of droplets against thermal cycling. While the use of fluorinated oil or supplementation of surfactant could improve the stability of droplets, this process has also greatly increased the cost of ddPCR and limited post-PCR analysis. Here, we report a novel method known as gel capsule-based digital PCR (gc-dPCR) which includes method to prepare hydrogel capsules encapsulating PCR reaction mix, conducting PCR reaction, and readout by either qPCR system or fluorescence microplate reader. We have compared our method to existing methods, i.e., quantitative PCR or vortex ddPCR. Our approach results in higher fluorescence intensity compared to ddPCR suggesting higher sensitivity of the system. As hydrogel capsules are more stable than droplets in fluorinated oil throughout thermal cycling, all partitions can be quantified, thus preventing loss of information from low-concentration samples. Our approach should extend to all droplet-based PCR methods. Generally, our approach has greatly improved ddPCR by increasing droplets stability and sensitivity, and reducing the cost of ddPCR, which help to remove the barrier of ddPCR in settings with limited resources. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/534823v2_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@15a291eorg.highwire.dtl.DTLVardef@4189e2org.highwire.dtl.DTLVardef@c35fd8org.highwire.dtl.DTLVardef@c972d0_HPS_FORMAT_FIGEXP M_FIG C_FIG